recombinant organisms are provided comprising genes encoding a glycerol-3-phosphate dehydrogenase and/or a glycerol-3-phosphatase activity useful for the production of glycerol from a variety of carbon substrates.
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1. A method for the production of glycerol from a recombinant microorganism comprising:
(i) transforming a suitable host cell with an expression cassette comprising (a) a gene encoding a nadh-dependent glycerol-3-phosphate dehydrogenase enzyme or a NADPH-dependent glycerol-3-phosphate dehydrogenase enzyme; and (b) a gene encoding a polypeptide encoding a glycerol-3-phosphatase (EC 3.1.3.21) enzyme; (ii) culturing the transformed host cell of (i) in the presence of at least one carbon source selected from the group consisting of monosaccharides, oligosaccharides, polysaccharides, and single-carbon substrates, whereby glycerol is produced; and (iii) recovering the glycerol produced in (ii).
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This application is a national filing of PCT/US97/20293, filed internationally Nov. 10, 1997, which in turn claims benefit of US Provisional application 60/030,602, filed Nov. 13, 1996.
The present invention relates to the field of molecular biology and the use of recombinant organisms for the production of desired compounds. More specifically it describes the expression of cloned genes for glycerol-3-phosphate dehydrogenase (G3PDH) and glycerol-3-phosphatase (G3P phosphatase), either separately or together, for the enhanced production of glycerol.
Glycerol is a compound in great demand by industry for use in cosmetics, liquid soaps, food, pharmaceuticals, lubricants, anti-freeze solutions, and in numerous other applications. The esters of glycerol are important in the fat and oil industry.
Not all organisms have a natural capacity to synthesize glycerol. However, the biological production of glycerol is known for some species of bacteria, algae, and yeasts. The bacteria Bacillus licheniformis and Lactobacillus lycopersica synthesize glycerol. Glycerol production is found in the halotolerant algae Dunaliella sp. and Asteronmonas gracilis for protection against high external salt concentrations (Ben-Amotz et al., (1982) Experientia 38:49-52). Similarly, various osmotolerant yeasts synthesize glycerol as a protective measure. Most strains of Saccharomyces produce some glycerol during alcoholic fermentation, and this can be increased physiologically by the application of osmotic stress (Albertyn et al., (1994) Mol. Cell. Biol. 14, 4135-4144). Earlier this century glycerol was produced commercially with Saccharomyces cultures to which steering reagents were added such as sulfites or alkalis. Through the formation of an inactive complex, the steering agents block or inhibit the conversion of acetaldehyde to ethanol, thus, excess reducing equivalents (NADH) are available to or "steered" towards dihydroxyacetone phosphate (DHAP) for reduction to produce glycerol. This method is limited by the partial inhibition of yeast growth that is due to the sulfites. This limitation can be partially overcome by the use of alkalis which create excess NADH equivalents by a different mechanism. In this practice, the alkalis initiated a Cannizarro disproportionation to yield ethanol and acetic acid from two equivalents of acetaldehyde.
The gene encoding glycerol-3-phosphate dehydrogenase (DAR1,GPD1) has been cloned and sequenced from Sacchatromyces diastaticus (Wang et al., (1994). J. Bact. 176:7091-7095). The DAR1 gene was cloned into a shuttle vector and used to transform E. coli where expression produced active enzyme. Wang et al., supra recognizes that DAR1 is regulated by the cellular osmotic environment but does not suggest how the gene might be used to enhance glycerol production in a recombinant organism.
Other glycerol-3-phosphate dehydrogenase enzymes have been isolated. For example, sn-glycerol-3-phosphate dehydrogenase has been cloned and sequenced from S. cerevisiae (Larason et al., (1993) Mol. Microbiol., 10:1101, (1993)). Albertyn et al., (1994) Mol. Cell. Biol., 14:4135) teach the cloning of GPD1 encoding a glycerol-3-phosphate dehydrogenase from S. cerevisiae. Like Wang et al., both Albertyn et al., and Larason et al. recognize the osmo-sensitivity of the regulation of this gene but do not suggest how the gene might be used in the production of glycerol in a recombinant organism.
As with G3DPH, glycerol-3-phosphatase has been isolated from Saccharomyces cerevisiae and the protein identified as being encoded by the GPP1 and GPP2 genes (Norbeck et al., (1996) J. Biol. Chem., 271:13875). Like the genes encoding G3DPH, it appears that GPP2 is osmotically-induced.
There is no known art that teaches glycerol production from recombinant organisms with G3PDH/G3P phosphatase expressed together or separately. Nor is there known art that teaches glycerol production from any wild-type organism with these two enzyme activities that does not require applying some stress (salt or an osmolyte) to the cell. Eustace ((1987), Can. J. Microbiol., 33:112-117)) teaches away from achieving glycerol production by recombinant DNA techniques. By selective breeding techniques, these investigators created a hybridized yeast strain that produced glycerol at greater levels than the parent strains: however, the G3PDH activity remained constant or slightly lower.
A microorganism capable of producing glycerol under physiological conditions is industrially desirable, especially when the glycerol itself will be used as a substrate in vivo as part of a more complex catabolic or biosynthetic pathway that could be perturbed by osmotic stress or the addition of steering agents.
The problem to be solved, therefore, is how to direct carbon flux towards glycerol production by the addition or enhancement of certain enzyme activities, especially G3PDH and G3P phosphatase which respectively catalyze the conversion of dihydroxyacetone phosphate (DHAP) to glycerol-3-phosphate (G3P) and then to glycerol. This process has not previously been described for a recombinant organism and required the isolation of genes encoding the two enzymes and their subsequent expression. A surprising and unanticipated difficulty encountered was the toxicity of G3P phosphatase to the host which required careful control of its expression levels to avoid growth inhibition.
The present invention provides a method for the production of glycerol from a recombinant organism comprising: (i) transforming a suitable host cell with an expression cassette comprising either or both
(a) a gene encoding a glycerol-3-phosphate dehydrogenasc enzyme;
(b) a gene encoding a glycerol-3-phosphate phosphatase enzyme: (ii) culturing the transformed host cell in the presence of at least one carbon source selected from the group consisting of monosaccharides, oligosaccharides. polysaccharides, and single-carbon substrates, or mixtures thereof whereby glycerol is produced; and (iii) recovering the glycerol. Glucose is the most preferred carbon source.
The invention further provides transformed host cells comprising expression cassettes capable of expressing glycerol-3-phosphate dehydrogenase and glycerol-3-phosphatase activities for the production of glycerol.
Applicants have made the following biological deposits under the terms of the Budapest Treaty on the International Recognition of the Deposit of Micro-organisms for the Purposes of Patent Procedure:
| Depositor Identification | Int'l. Depository | |
| Reference | Designation | Date of Deposit |
| Escherichia coli pAH21/DH5α | ATCC 98187 | 26 September |
| (containing the GPP2 gene) | 1996 | |
| Escherichia coli (pDAR1A/AA200) | ATCC 98248 | 6 November |
| (containing the DAR1 gene) | 1996 | |
"ATCC" refers to the American Type Culture Collection international depository located at 12301 Parklawn Drive Rockville, Md. 20852 U.S.A. The designation is the accession number of the deposited material.
Applicants have provided 23 sequences in conformity with the Rules for the Standard Representation of Nucleotide and Amino Acid Sequences in Patent Applications (Annexes I and II to the Decision of the President of the EPO, published in Supplement No. 2 to OJ EPO. 12/1992) and with 37 C.F.R. 1.821-1.825 and Appendices A and B (Requirements for Application Disclosures Containing Nucleotides and/or Amino Acid Sequences).
The present invention provides a method for the biological production of glycerol from a fermentable carbon source in a recombinant organism. The method provides a rapid inexpensive and environmentally-responsible source of glycerol useful in the cosmetics and pharmaceutical industries. The method uses a microorganism containing cloned homologous or heterologous genes encoding glycerol-3-phosphate dehydrogenase (G3PDH) and/or glycerol-3-phosphatase (G3P phosphatase). The microorganism is contacted with a carbon source and glycerol is isolated from the conditioned media. The genes may be incorporated into the host microorganism separately or together for the production of glycerol.
As used herein the following terms may be used for interpretation of the claims and specification.
The terms "glycerol-3-phosphate dehydrogenase" and "G3PDH" refer to a polypeptide responsible for an enzyme activity that catalyzes the conversion of dihydroxyacetone phosphate (DHAP) to glycerol-3-phosphate (G3P). In vivo G3PDH may be NADH, NADPH; or FAD-dependent. The NADH-dependent enzyme (EC 1.1.1.8) is encoded by several genes including GPD1 (GenBank Z74071×2), or GPD2 (GenBank Z35169×1), or GPD3 (GenBank G984182), or DAR1 (GenBank Z74071×2). The NADPH-dependent enzyme (EC 1.1.1.94) is encoded by gpsA (GenBank U321643, (cds 197911-196892) G466746 and L45246). The FAD-dependent enzyme (EC 1.1.99.5) is encoded by GUT2 (GenBank Z47047×23), or glpD (GenBank G147838), or glpABC (GenBank M20938).
The terms "glycerol-3-phosphate phosphatase", "sn-glycerol-3-phosphatase", or "d,l-glycerol phosphatase", and "G3P phosphatase" refer to a polypeptide responsible for an enzyme activity that catalyzes the conversion of glycerol-3-phosphate to glycerol. G3P phosphatase is encoded by GPP1 (GenBank Z47047×125), or GPP2 (GenBank U18813×11).
The term "glycerol kinase" refers to a polypeptide responsible for an enzyme activity that catalyzes the conversion of glycerol to glycerol-3-phosphate, or glycerol-3-phosphate to glycerol, depending on reaction conditions. Glycerol kinase is encoded by GUT1 (GenBank U11583×9).
The terms "GPD1", "DAR1", "OSG1", "D2830" and "YDL022W" will be used interchangeably and refer to a gene that encodes a cytosolic glycerol-3-phosphate dehydrogenase and is characterized by the base sequence given as SEQ ID NO:1.
The term "GPD2" refers to a gene that encodes a cytosolic glycerol-3-phosphate dehydrogenase and is characterized by the base sequence given in SEQ ID NO:2.
The terms "GUT2" and "YIL155C" are used interchangeably and refer to a gene that encodes a mitochondrial glycerol-3-phosphate dehydrogenase and is characterized by the base sequence given in SEQ ID NO:3.
The terms "GPP1", "RHR2" and "YIL053W" are used interchangeably and refer to a gene that encodes a cytosolic glycerol-3-phosphatase and is characterized by the base sequence given in SEQ ID NO:4.
The terms "GPP2", "HOR2" and "YER062C" are used interchangeably and refer to a gene that encodes a cytosolic glycerol-3-phosphatase and is characterized by the base sequence given as SEQ ID NO:5.
The term "GUT1" refers to a gene that encodes a cytosolic glycerol kinase and is characterized by the base sequence given as SEQ ID NO:6.
As used herein, the terms "function" and "enzyme function" refer to the catalytic activity of an enzyme in altering the energy required to perform a specific chemical reaction. Such an activity may apply to a reaction in equilibrium where the production of both product and substrate may be accomplished under suitable conditions.
The terms "polypeptide" and "protein" are used herein interchangeably.
The terms "carbon substrate" and "carbon source" refer to a carbon source capable of being metabolized by host organisms of the present invention and particularly mean carbon sources selected from the group consisting of monosaccharides, oligosaccharides, polysaccharides, and one-carbon substrates or mixtures thereof.
The terms "host cell" and "host organism" refer to a microorganism capable of receiving foreign or heterologous genes and expressing those genes to produce an active gene product.
The terms "foreign gene", "foreign DNA", "heterologous gene", and "heterologous DNA" all refer to genetic material native to one organism that has been placed within a different host organism.
The terms "recombinant organism" and "transformed host" refer to any organism transformed with heterologous or foreign genes. The recombinant organisms of the present invention express foreign genes encoding G3PDH and G3P phosphatase for the production of glycerol from suitable carbon substrates.
"Gene" refers to a nucleic acid fragment that expresses a specific protein, including regulatory sequences preceding (5' non-coding) and following (3' non-coding) the coding region. The terms "native" and "wild-type" gene refer to the gene as found in nature with its own regulatory sequences.
As used herein, the terms "encoding" and "coding" refer to the process by which a gene, through the mechanisms of transcription and translation, produces an amino acid sequence. The process of encoding a specific amino acid sequence is meant to include DNA sequences that may involve base changes that do not cause a change in the encoded amino acid, or which involve base changes which may alter one or more amino acids, but do not affect the functional properties of the protein encoded by the DNA sequence. Therefore, the invention encompasses more than the specific exemplary sequences. Modifications to the sequence, such as deletions, insertions, or substitutions in the sequence which produce silent changes that do not substantially affect the functional properties of the resulting protein molecule are also contemplated. For example, alterations in the gene sequence which reflect the degeneracy of the genetic code, or which result in the production of a chemically equivalent amino acid at a given site, are contemplated: thus, a codon for the amino acid alanine, a hydrophobic amino acid, may be substituted by a codon encoding another less hydrophobic residue, such as glycine, or a more hydrophobic residue, such as valine, leucine, or isoleucine. Similarly, changes which result in substitution of one negatively charged residue for another, such as aspartic acid for glutamic acid, or one positively charged residue for another, such as lysine for arginine, can also be expected to produce a biologically equivalent product. Nucleotide changes which result in alteration of the N-terminal and C-terminal portions of the protein molecule would also not be expected to alter the activity of the protein. In some cases, it may in fact be desirable to make mutants of the sequence in order to study the effect of alteration on the biological activity of the protein. Each of the proposed modifications is well within the routine skill in the art, as is determination of retention of biological activity in the encoded products. Moreover, the skilled artisan recognizes that sequences encompassed by this invention are also defined by their ability to hybridize, under stringent conditions (0.1×SSC, 0.1% SDS, 65°C C.), with the sequences exemplified herein.
The term "expression" refers to the transcription and translation to gene product from a gene coding for the sequence of the gene product.
The terms "plasmid", "vector", and "cassette" as used herein refer to an extra chromosomal element often carrying genes which are not part of the central metabolism of the cell and usually in the form of circular double-stranded DNA molecules. Such elements may be autonomously replicating sequences, genome integrating sequences, phage or nucleotide sequences, linear or circular, of a single- or double-stranded DNA or RNA, derived from any source, in which a number of nucleotide sequences have been joined or recombined into a unique construction which is capable of introducing a promoter fragment and DNA sequence for a selected gene product along with appropriate 3' untranslated sequence into a cell. "Transformation cassette" refers to a specific vector containing a foreign gene and having elements in addition to the foreign gene that facilitate transformation of a particular host cell. "Expression cassette" refers to a specific vector containing a foreign gene and having elements in addition to the foreign gene that allow for enhanced expression of that gene in a foreign host.
The terms "transformation" and "transfection" refer to the acquisition of new genes in a cell after the incorporation of nucleic acid. The acquired genes may be integrated into chromosomal DNA or introduced as extrachromosomal replicating sequences. The term "transformant" refers to the cell resulting from a transformation.
The term "genetically altered" refers to the process of changing hereditary material by transformation or mutation.
It is contemplated that glycerol may be produced in recombinant organisms by the manipulation of the glycerol biosynthetic pathway found in most microorganisms. Typically, a carbon substrate such as glucose is converted to glucose-6-phosphate via hexokinase in the presence of ATP. Glucose-phosphate isomerase catalyzes the conversion of glucose-6-phosphate to fructose-6-phosphate and then to fructose-1,6-diphosphate through the action of 6-phosphofructokinase. The diphosphate is then taken to dihydroxyacetone phosphate (DHAP) via aldolase. Finally NADH-dependent G3PDH converts DHAP to glycerol-3-phosphate which is then dephosphorylated to glycerol by G3P phosphatase. (Agarwal (1990), Adv. Biochem. Engrg. 41:114).
An alternative pathway for glycerol production from DHAP has been suggested (Wang et al., (1994) J. Bact. 176:7091-7095). In this proposed pathway DHAP could be dephosphorylated by a specific or non-specific phosphatase to give dihydroxyacetone, which could then be reduced to glycerol by a dihydroxy-acetone reductase. Dihydroxyacetone reductase is known in prokaryotes and in Schizosaccharomyces pombe, and cloning and expression of such activities together with an appropriate phosphatase could lead to glycerol production. Another alternative pathway for glycerol production from DHAP has been suggested (Redkar (1995), Experimental Mycology, 19:241, 1995). In this pathway DHAP is isomerized to glyceraldehyde-3-phosphate by the common glycolytic enzyme triose phosphate isomerase. Glyceraldehyde-3-phosphate is dephosphorylated to glyceraldehyde, which is then reduced by alcohol dehydrogenase or a NADP-dependent glycerol dehydrogenase activity. The cloning and expression of the phosphatase and dehydrogenase activities from Aspergillus nidulans could lead to glycerol production.
The present invention provides genes suitable for the expression of G3PDH and G3P phosphatase activities in a host cell.
Genes encoding G3PDH are known. For example, GPD1 has been isolated from Saccharomyces and has the base sequence given by SEQ ID NO:1. encoding the amino acid sequence given in SEQ ID NO:7 (Wang et al., supra). Similarly, G3PDH activity has also been isolated from Saccharomyces encoded by GPD2 having the base sequence given in SEQ ID NO:2 encoding the amino acid sequence given in SEQ ID NO:8 (Eriksson et al., (1995) Mol. Microbiol., 17:95).
For the purposes of the present invention it is contemplated that any gene encoding a polypeptide responsible for G3PDH activity is suitable wherein that activity is capable of catalyzing the conversion of dihydroxyacetone phosphate (DHAP) to glycerol-3-phosphate (G3P). Further, it is contemplated that any gene encoding the amino acid sequence of G3PDH as given by SEQ ID NOS:7, 8, 9, 10, 11 and 12 corresponding to the genes GPD1, GPD2, GUT2, gpsA, glpD, and the α subunit of glpABC respectively, will be functional in the present invention wherein that amino acid sequence may encompass amino acid substitutions, deletions or additions that do not alter the function of the enzyme. The skilled person will appreciate that genes encoding G3PDH isolated from other sources will also be suitable for use in the present invention. For example, genes isolated from prokaryotes include GenBank accessions M34393, M20938, L06231, U12567, L45246, L45323, L45324, L45325, U32164, U32689, and U39682. Genes isolated from fungi include GenBank accessions U30625, U30876 and X56162; genes isolated from insects include GenBank accessions X61223 and X14179; and genes isolated from mammalian sources include GenBank accessions U12424, M25558 and X78593.
Genes encoding G3P phosphatase are known. For example, GPP2 has been isolated from Saccharomyces cerevisiae and has the base sequence given by SEQ ID NO:5, which encodes the amino acid sequence (given in SEQ ID NO:13 (Norbeck et al., (1996), J. Biol. Chem., 271:13875).
For the purposes of the present invention, any gene encoding a G3P phosphatase activity is suitable for use in the method wherein that activity is capable of catalyzing the conversion of glycerol-3-phosphate to glycerol. Further, any gene encoding the amino acid sequence of G3P phosphatase as given by SEQ ID NOS:13 and 14 corresponding to the genes GPP2 and GPP1 respectively, will be functional in the present invention including any amino acid sequence that encompasses amino acid substitutions, deletions or additions that do not alter the function of the G3P phosphatase enzyme. The skilled person will appreciate that genes encoding G3P phosphatase isolated from other sources will also be suitable for use in the present invention. For example, the dephosphorylation of glycerol-3-phosphate to yield glycerol may be achieved with one or more of the following general or specific phosphatases: alkaline phosphatase (EC 3.1.3.1) [GenBank M19159, M29663, U02550 or M339651]; acid phosphatase (EC 3.1.3.2) [GenBank U51210, U19789, U28658 or L205661]; glycerol-3-phosphatase (E.C. 3.1.3.21) [GenBank Z38060 or U18813×11]; glucose-1-phosphatase (EC 3.1.3.10) [GenBank M338071]; glucose-6-phosphatase (EC 3.1.3.9) [GenBank U00445]; fructose-1,6-bisphosphatase (EC 3.1.3.11) [GenBank X12545 or J03207] or phosphotidyl glycerol phosphate phosphatase (EC 3.1.3.27) [GenBank M23546 and M23628].
Genes encoding glycerol kinase are known. For example. GUT1 encoding the glycerol kinase from Saccharomyces has been isolated and sequenced (Pavlik et al. (1993), Curr. Genet., 24:21) and the base sequence is given by SEQ ID NO:6, which encodes the amino acid sequence given in SEQ ID NO:15. The skilled artisan will appreciate that, although glycerol kinase catalyzes the degradation of glycerol in nature, the same enzyme will be able to function in the synthesis of glycerol, converting glycerol-3-phosphate to glycerol under the appropriate reaction energy conditions. Evidence exists for glycerol production through a glycerol kinase. Under anaerobic or respiration-inhibited conditions, Trypanosoma brucei gives rise to glycerol in the presence of Glycerol-3-P and ADP. The reaction occurs in the glycosome compartment (Hammond, (1985), J. Biol. Chem., 260:15646-15654).
Suitable host cells for the recombinant production of glycerol by the expression of G3PDH and G3P phosphatase may be either prokaryotic or eukaryotic and will be limited only by their ability to express active enzymes. Preferred host cells will be those bacteria, yeasts, and filamentous fungi typically useful for the production of glycerol such as Citriobacter, Enterobacter, Clostridium, Klebsiella, Aerobactet, Lactobacillus, Aspergillus, Saccharomyces, Schizosaccharomyces, Zygosaccharomyces, Pichia, Kluyveromyces. Candida, Hansenula, Debaryomyces. Mucor, Torulopsis, Methylobacter, Escherichia, Salmonella, Bacillus, Streptomyces and Pseudomnonas. Preferred in the present invention are E. coli and Saccharomyces.
The present invention provides a variety of vectors and transformation and expression cassettes suitable for the cloning, transformation and expression of G3PDH and G3P phosphatase into a suitable host cell. Suitable vectors will be those which are compatible with the bacterium employed. Suitable vectors can be derived, for example, from a bacteria, a virus (such as bacteriophage T7 or a M-13 derived phage), a cosmid, a yeast or a plant. Protocols for obtaining and using such vectors are known to those in the art (Sambrook et al., Molecular Cloning: A Laboratory Manual--volumes 1, 2, 3 (Cold Spring Harbor laboratory: Cold Spring Harbor, N.Y., 1989)).
Typically, the vector or cassette contains sequences directing transcription and translation of the appropriate gene, a selectable marker, and sequences allowing autonomous replication or chromosomal integration. Suitable vectors comprise a region 5' of the gene which harbors transcriptional initiation controls and a region 3' of the DNA fragment which controls transcriptional termination. It is most preferred when both control regions are derived from genes homologous to the transformed host cell. Such control regions need not be derived from the genes native to the specific species chosen as a production host.
Initiation control regions or promoters, which are useful to drive expression of the G3PDH and G3P phosphatase genes in the desired host cell are numerous and familiar to those skilled in the art. Virtually any promoter capable of driving these genes is suitable for the present invention including but not limited to CYC1, HIS3, GAL1, GAL10, ADH1, PGK, PHO5, GAPDH, ADC1, TRP1, URA3, LEU2, ENO, and TPI (useful for expression in Saccharomyces); AOX1 (useful for expression in Pichia); and lac, trp, λPL, λPR, T7, tac, and trc, (useful for expression in E. coli).
Termination control regions may also be derived from various genes native to the preferred hosts. Optionally, a termination site may be unnecessary; however, it is most preferred if included.
For effective expression of the instant enzymes, DNA encoding the enzymes are linked operably through initiation codons to selected expression control regions such that expression results in the formation of the appropriate messenger RNA.
Once suitable cassettes are constructed they are used to transform appropriate host cells. Introduction of the cassette containing the genes encoding G3PDH and/or G3P phosphatase into the host cell may be accomplished by known procedures such as by transformation, e.g., using calcium-permeabilized cells, electroporation, or by transfection using a recombinant phage virus (Sambrook et al., supra).
In the present invention AH21 and DAR1 cassettes were used to transform the E. coli DH5α as fully described in the GENERAL METHODS and EXAMPLES.
Fermentation media in the present invention must contain suitable carbon substrates. Suitable substrates may include but are not limited to monosaccharides such as glucose and fructose, olioosaecharides such as lactose or sucrose, polysaccharides such as starch or cellulose or mixtures thereof and unpurified mixtures from renewable feedstocks such as cheese whey permeate, cornsteep liquors sugar beet molasses, and barley malt. Additionally, the carbon substrate may also be one-carbon substrates such as carbon dioxide, or methanol for which metabolic conversion into key biochemical intermediates has been demonstrated.
Glycerol production from single carbon sources (e.g., methanol, formaldehyde or formate) has been reported in methylotrophic yeasts (Yamada et al. (1989), Agric. Biol. Chem., 53(2):541-543) and in bacteria (Hunter et al. (1985), Biochemistry, 24:4148-4155). These organisms can assimilate single carbon compounds, ranging in oxidation state from methane to formate, and produce glycerol. The pathway of carbon assimilation can be through ribulose monophosphate, through serine, or through xylulose-monophosphate (Gottschalk. Bacterial Metabolism, Second Edition, Springer-Verlag: New York (1986)). The ribulose monophosphate pathway involves the condensation of formate with ribulose-5-phosphate to form a 6 carbon sugar that becomes fructose and eventually the three carbon product. glyceraldehyde-3-phosphate. Likewise, the serine pathway assimilates the one-carbon compound into the glycolytic pathway via methylenetetrahydrofolate.
In addition to one and two carbon substrates, methylotrophic organisms are also known to utilize a number of other carbon-containing compounds such as methylamine, glucosamine and a variety of amino acids for metabolic activity. For example. methylotrophic yeast are known to utilize the carbon from methylamine to form trehalose or glycerol (Bellion et al. (1993), Microb. Growth Cl Compd., [Int. Symp.], 7th, 415-32. Editor(s): Murrell, J. Collin; Kelly, Don P. Publisher: Intercept, Andover, UK). Similarly, various species of Candida will metabolize alanine or oleic acid (Sulter et al. (1990), Arch. Microbiol., 153(5):485-9). Hence, the source of carbon utilized in the present invention may encompass a wide variety of carbon-containing substrates and will only be limited by the choice of organism.
Although all of the above mentioned carbon substrates and mixtures thereof are suitable in the present invention, preferred carbon substrates are monosaccharides, oligosaccharides, polysaccharides, single-carbon substrates or mixtures thereof. More preferred are sugars such as glucose, fructose, sucrose, maltose, lactose and single carbon substrates such as methanol and carbon dioxide. Most preferred as a carbon substrate is glucose.
In addition to an appropriate carbon source, fermentation media must contain suitable minerals, salts, cofactors, buffers and other components, known to those skilled in the art, suitable for the growth of the cultures and promotion of the enzymatic pathway necessary for glycerol production.
Typically cells are grown at 30°C C. in appropriate media. Preferred growth media are common commercially prepared media such as Luria Bertani (LB) broth, Sabouraud Dextrose (SD) broth, or Yeast medium (YM) broth. Other defined or synthetic growth media may also be used and the appropriate medium for growth of the particular microorganism will be known by one skilled in the art of microbiology or fermentation science. The use of agents known to modulate catabolite repression directly or indirectly, e.g., cyclic adenosine 2':3'-mono-phosphate, may also be incorporated into the reaction media. Similarly, the use of agents known to modulate enzymatic activities (e.g., sulfites, bisulfites, and alkalis) that lead to enhancement of glycerol production may be used in conjunction with or as an alternative to genetic manipulations.
Suitable pH ranges for the fermentation are between pH 5.0 to pH 9.0 where the range of pH 6.0 to pH 8.0 is preferred for the initial condition.
Reactions may be performed under aerobic or anaerobic conditions where anaerobic or microaerobic conditions are preferred.
The levels of expression of the proteins G3PDH and G3P phosphatase are measured by enzyme assays. G3PDH activity assay relies on the spectral properties of the cosubstrate, NADH, in the DHAP conversion to G-3-P. NADH has intrinsic UV/vis absorption and its consumption can be monitored spectro-photometrically at 340 nm. G3P phosphatase activity can be measured by any method of measuring the inorganic phosphate liberated in the reaction. The most commonly used detection method uses the visible spectroscopic determination of a blue-colored phosphomolybdate ammonium complex.
Glycerol may be identified and quantified by high performance liquid chromatography (HPLC) and gas chromatography/mass spectroscopy (GC/MS) analyses on the cell-free extracts. Preferred is a method where the fermentation media are analyzed on an analytical ion exchange column using a mobile phase of 0.1N sulfuric acid in an isocratic fashion.
Methods for the recovery of glycerol from fermentation media are known in the art. For example, glycerol can be obtained from cell media by subjecting the reaction mixture to the following sequence of steps: filtration; water removal; organic solvent extraction, and fractional distillation (U.S. Pat. No. 2,986,495).
In the absence of a functional gpsA-encoded G3PDH, E. coli cells are unable to synthesize G3P, a condition which leads to a block in membrane biosynthesis. Cells with such a block are auxotrophic, requiring that either glycerol or G3P be present in the culture media for synthesis of membrane phospholipids.
A cloned heterologous wild-type gpsA gene is able to complement the chromosomal gpsA mutation to allow growth in media lacking glycerol or G3P (Wang, et al. (1994), J. Bact. 176:7091-7095). Based on this complementation strategy, growth of gpsA-defective cells on glucose would only occur if they possessed a plasmid-encoded gpsA, allowing a selection based on synthesis of G3P from DHAP. Cells which lose the recombinant gpsA plasmid during culture would fail to synthesize G3P and cell growth would subsequently be inhibited. The complementing G3PDH activity can be expressed not only from gpsA, but also from other cloned genes expressing G3PDH activity such as GPD1, GPD2, GPD3, GUT2, glpD, and glpABC. These can be maintained in a gpsA-defective E. coli strain such as BB20 (Cronan et al. (1974), J. Bact., 118:598), alleviating the need to use antibiotic selection and its prohibitive cost in large-scale fermentations.
A related strategy can be used for expression and selection in osmoregulatory mutants of S. cerevisiae (Larsson et al. (1993), Mol. Microbiol., 10:1101-1111). These osg1 mutants are unable to grow at low water potential and show a decreased capacity for glycerol production and reduced G3PDH activity. The osg1 salt sensitivity defect can be complemented by a cloned and expressed G3PDH gene. Thus, the ability to synthesize glycerol can be used simultaneously as a selection marker for the desired glycerol-producing cells.
Procedures for phosphorylations ligations and transformations are well known in the art. Techniques suitable for use in the following examples may be found in Sambrook et al., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press (1989).
Materials and methods suitable for the maintenance and growth of bacterial cultures are well known in the art. Techniques suitable for use in the following examples may be found in Manual of Methods for General Bacteriology (Phillipp Gerhardt. R. G. E. Murray, Ralph N. Costilow, Eugene W. Nester. Willis A. Wood, Noel R. Krieg and G. Briggs Phillips eds), American Society for Microbiology, Washington, DC. (1994) or in Biotechnology: A Textbook of Industrial Microbioloy (Thomas D. Brock, Second Edition (1989) Sinauer Associates. Inc., Sunderland. Mass.). All reagents and materials used for the growth and maintenance of bacterial cells were obtained from Aldrich Chemicals (Milwaukee, Wis.), DIFCO Laboratories (Detroit, Mich.), GIBCO/BRL (Gaithersburg, Md.), or Sigma Chemical Company (St. Louis. Mo.) unless otherwise specified.
The meaning of abbreviations is as follows: "h" means hour(s), "min" means minute(s), "sec" means second(s), "d" means day(s), "mL" means milliliters, "L" means liters.
The following Escherichia coli strains were used for transformation and expression of G3PDH and G3P phosphatase. Strains were obtained from the E. coli Genetic Stock Center or from Life Technologies, Gaithersburg, Md.).
AA200 (garB10 fhuA22 ompF627 fadL701 relA1 pit-10 spoT1 tpi-1 phoM510 mcrB1) (Anderson et al., (1970), J. Gen. Microbiol., 62:329).
BB20 (tonA22 ΔphoA8 fadL701 relA1 glpR2 glpD3 pit-10 gpsA20 spoT1 T2R) (Cronan et al., J. Bact., 118:598).
DH5α (deoR endA1 gyrA96 hsdR17 recA1 relA1 supE44 thi-1 Δ(lacZYA-a)gFV169) phi80lacZΔM15 F-) (Woodcock et al., (1989), Nucl. Acids Res. 17:3469).
The conversion of glucose to glycerol was monitored by IIPLC and/or GC. Analyses were performed using standard techniques and materials available to one of skill in the art of chromatography. One suitable method utilized a Waters Maxima 820 HPLC system using UV (210 nm) and RI detection. Samples were injected onto a Shodex SH-1011 column (8 mm×300 mm; Waters. Milford, Mass.) equipped with a Shodex SH-1011P precolumn (6 mm×50 mm), temperature-controlled at 50°C C., using 0.01 N H2SO4 as mobile phase at a flow rate of 0.5 mL/min. When quantitative analysis was desired, samples were injected onto a Shodex SH-1011 column (8 mm×300 mm: Waters, Milford, Mass.) equipped with a Shodex SH-1011P precolumn (6 mm×50 mm), temperature-controlled at 50°C C., using 0.01 N H2SO4 as mobile phase at a flow rate of 0.69 mL/min. When quantitative analysis was desired, samples were prepared with a known amount of trimethylacetic acid as an external standard. Typically, the retention times of glycerol (RI detection) and glucose (RI detection) were 17.03 min and 12.66 min. respectively.
Glycerol was also analyzed by GC/MS. Gas chromatography with mass spectrometry detection for and quantitation of glycerol was done using a DB-WAX column (30 m. 0.32 mm I.D., 0.25 um film thickness, J & W Scientific, Folsom, Calif.), at the following conditions: injector: split, 1:15; sample volume: 1 uL; temperature profile: 150°C C. intitial temperature with 30 sec hold, 40°C C./min to 180°C C., 20°C C./min to 240°C C. hold for 2.5 min. Detection: El Mass Spectrometry (Hewlett Packard 5971, San Fernando, Calif.), quantitative SIM using ions 61 m/z and 64 m/z as target ions for glycerol and glycerol-d8, and ion 43 m/z as qualifier ion for glycerol. Glycerol-d8 was used as an internal standard.
The assay for enzyme activity was performed by incubating the extract with an organic phosphate substrate in a bis-Tris or MES and magnesium buffer, pH 6.5. The substrate used was either 1-α-glycerol phosphate, or d,1-α-glycerol phosphate. The final concentrations of the reagents in the assay are: buffer (20 mM, bis-Tris or 50 mM MES); MgCl2 (10 mM); and substrate (20 mM). If the total protein in the sample was low and no visible precipitation occurs with an acid quench, the sample was conveniently assayed in the cuvette. This method involved incubating an enzyme sample in a cuvette that contained 20 mM substrate (50 μL, 200 mM), 50 mM MES, 10 mM MgCl2, pH 6.5 buffer. The final phosphatase assay volume was 0.5 mL. The enzyme-containing sample was added to the reaction mixture: the contents of the cuvette were mixed and then the cuvette was placed in a circulating water bath at T=37°C C. for 5 to 120 min, the length of time depending on whether the phosphatase activity in the enzyme sample ranged from 2 to 0.02 U/mL. The enzymatic reaction was quenched by the addition of the acid molybdate reagent (0.4 mL). After the Fiske SubbaRow reagent (0.1 mL) and distilled water (1.5 mL) were added, the solution was mixed and allowed to develop. After 10 min, to allow full color development, the absorbance of the samples was read at 660 nm using a Cary 219 UV/Vis spectrophotometer. The amount of inorganic phosphate released was compared to a standard curve that was prepared by using a stock inorganic phosphate solution (0.65 mM) and preparing 6 standards with final inorganic phosphate concentrations ranging from 0.026 to 0.130 μmol/mL.
The following procedure was used as modified below from a method published by Bell et al. (1975), J. Biol. Chem., 250:7153-8. This method involved incubating an enzyme sample in a cuvette that contained 0.2 mM NADH, 2.0 mM Dihydroxyacetone phosphate (DHAP), and enzyme in 0.1 M Tris/HCl, p1I 7.5 buffer with 5 mM DTT, in a total volume of 1.0 mL at 30°C C. The spectrophotometer was set to monitor absorbance changes at the fixed wavelength of 340 nm. The instrument was blanked on a cuvette containing buffer only. After the enzyme was added to the cuvette, an absorbance reading was taken. The first substrate, NADH (50 uL 4 mM NADH; absorbance should increase approx 1.25 AU), was added to determine the background rate. The rate should be followed for at least 3 min. The second substrate. DHAP (50 uL 40 mM DHAP). was then added and the absorbance change over time was monitored for at least 3 min to determine to determine the gross rate. G3PDH activity was defined by subtracting the background rate from the gross rate.
The Saccharomyces cerevisiae chromosome V lamda clone 6592 (Gene Bank, accession # U18813×11) was obtained from ATCC. The glycerol 3-phosphate phosphatase (GPP2) gene was cloned by cloning from the lamda clone as target DNA using synthetic primers (SEQ ID NO:16 with SEQ ID NO:17) incorporating an BamHI-RBS-XbaI site at the 5' end and a SmaI site at the 3' end. The product was subcloned into pCR-Script (Stratagene, Madison, Wis.) at the SrfI site to generate the plasmids pAH15 containing GPP2. The plasmid pAH 15 contains the GPP2 gene in the inactive orientation for expression from the lac promoter in pCR-Script SK+. The BamHI-SmaI fragment from pAH15 containing the GPP2 gene was inserted into pBlueScriptII SK+ to generate plasmid pAH 19. The pAH19 contains the GPP2 gene in the correct orientation for expression from the lac promoter. The XbaI-PstI fragment from pAH 19 containing the GPP2 gene was inserted into pPHOX2 to create plasmid pAH21. The pAH21/DH5α is the expression plasmid.
DAR1 was isolated by PCR cloning from genomic S. cerevisiae DNA using synthetic primers (SEQ ID NO:18 with SEQ ID NO:19). Successful PCR cloning places an NcoI site at the 5' end of DAR1 where the ATG within NcoI is the DAR1 initiator methionine. At the 3' end of DAR1 a BamHI site is introduced following the translation terminator. The PCR fragments were digested with NcoI +BamHI and cloned into the same sites within the expression plasmid pTrc99A (Pharmacia, Piscataway, N.J.) to give pDAR1A.
In order to create a better ribosome binding site at the 5' end of DAR1, an SpeI-RBS-NcoI linker obtained by annealing synthetic primers (SEQ ID NO:20 with SEQ ID NO:21) was inserted into the NcoI site of pDAR1A to create pAH40. Plasmid pAH40 contains the new RBS and DAR1 gene in the correct orientation for expression from the trc promoter of pTrc99A (Pharmacia, Piscataway, N.J.). The NcoI-BamHI fragment from pDAR1A and an second set of SpeI-RBS-NcoI linker obtained by annealing synthetic primers (SEQ ID NO:22 with SEQ ID NO:23) was inserted into the SpeI-BamHI site of pBC-SK+ (Stratagene, Madison, Wis.) to create plasmid pAH42. The plasmid pAH42 contains a chloramphenicol resistant gene.
Expression cassettes for DAR1 and GPP2 were assembled from the individual DAR1 and GPIP2 subclones described above using standard molecular biology methods. The BamHI-PstI fragment from pAH19 containing the ribosomal binding site (RBS) and GPP2 gene was inserted into pAH40 to create pAH43. The BamHI-PstI fragment from pAH19 containing the RBS and GPP2 gene was inserted into pAH42 to create pAH45.
The ribosome binding site at the 5' end of GPP2 was modified as follows. A BamHI-RBS-SpeI linker, obtained by annealing synthetic primers GATCCAGGAAACAGA (SEQ ID NO:24) with CTAGTCTGTTFTCCTG (SEQ ID NO:25) to the XbaI-PstI fragment from pAH19 containing the GPP2 gene, was inserted into the BamHI-PstI site of pAH40 to create pAH48. Plasmid pAH48 contains the DAR1 genes the modified RBS, and the GPP2 gene in the correct orientation for expression from the trc promoter of pTrc99A (Pharmacia Piscataway, N.J.).
All the plasmids described here were transformed into E. coli DH5α using standard molecular biology techniques. The transformants were verified by its DNA RFLP pattern.
Synthetic media was used for anaerobic or aerobic production of glycerol using E. coli cells transformed with pDAR1 A. The media contained per liter 6.0 g Na2HPO4, 3.0 g KH2PO4, 1.0 g NH4Cl, 0.5 g NaCl, 1 mL 20% MgSO4,7H2O, 8.0 g glucose, 40 mg casamino acids 0.5 ml 1% thiamine hydrochloride, 100 mg ampicillin.
Strain AA200 harboring pDAR1A or the pTrc99A vector was grown in aerobic conditions in 50 mL of media shaking at 250 rpm in 250 mL flasks at 37°C C. At A600 0.2-0.3 isopropylthio-β-D-galactoside was added to a final concentration of 1 mM and incubation continued for 48 h. For anaerobic growth samples of induced cells were used to fill Falcon #2054 tubes which were capped and gently mixed by rotation at 37°C C. for 48 h. Glycerol production was determined by HPLC analysis of the culture supernatants. Strain pDAR1A/AA200 produced 0.38 g/L glycerol after 48 h under anaerobic conditions, and 0.48 g/L under aerobic conditions.
Synthetic phoA media was used in shake flasks to demonstrate the increase of glycerol by GPP2 expression in E. coli. The phoA medium contained per liter: Amisoy, 12 g; ammonium sulfate. 0.62 g; MOPS, 10.5 g, Na-citrate, 1.2 g; NaOH (1 M), 10 mL. 1 M MgSO4, 12 mL; 100X trace elements, 12 mL; 50% glucose. 10 mL; 1% thiamine, 10 mL; 100 mg/mL L-proline, 10 mL, 2.5 mM FeCl3, 5 mL; mixed phosphates buffer, 2 mL (5 mL 0.2 M NaH2PO4+9 mL 0.2 M K2HPO4), and pH to 7∅ The 100X traces elements for phoA medium/L contained: ZnSO4.7 H2O, 0.58 g; MnSO4.H2O, 0.34 g; CuSO4.5 H2O, 0.49 g; CoCl2.6 H2O, 0.47 g: H3BO3, 0.12 g. NaMoO4.2 H2O, 0.48 g.
The strains pAH21/DH5α (containing GPP2 gene) and pPHOX2/DH5α (control) were grown in 45 mL of media (phoA media. 50 ug/mL carbenicillin, and 1 ug/mL vitamin B12) in a 250 mL shake flask at 37°C C. The cultures were grown under aerobic condition (250 rpm shaking) for 24 h. Glycerol production was determined by HPLC analysis of the culture supernatant. pAH21/DH5α produced 0.2 g/L glycerol after 24 h.
Growth for demonstration of increased glycerol production by E. coli DH5α-containing pAH43 proceeds aerobically at 37°C C. in shake-flask cultures (erlenmeyer flasks, liquid volume ⅕th of total volume).
Cultures in minimal media/1% glucose shake-flasks are started by inoculation from overnight LB/1% glucose culture with antibiotic selection. Minimal media are: filter-sterilized defined media, final pH 6.8 (HCl), contained per liter: 12.6 g (NH4)2SO4, 13.7 g K2HPO4, 0.2 g yeast extract (Difco), 1 g NaHCO3, 5 mg vitamin B12, 5 mL Modified Balch's Trace-Element Solution (the composition of which can be found in Methods for General and Molecular Bacteriology (P. Gerhardt et al., eds, p. 158, American Society for Microbiology, Washington, D.C. (1994)). The shake-flasks are incubated at 37°C C. with vigorous shaking for overnight, after which they are sampled for GC analysis of the supernatant. The pAH43/DH5α showed glycerol production of 3.8 g/L after 24 h.
Example 4 illustrates the production of glucose from the recombinant E. coli DH5α/pAH48, containing both the GPP2 and DAR1 genes.
The strain DH5a/pAH48 was constructed as described above in the
DH5α/pAH48 were pre-cultured for seeding into a fermentation run. Components and protocols for the pre-culture are listed below.
| Pre-Culture Media | |||
| KH2PO4 | 30.0 | g/L | |
| Citric acid | 2.0 | g/L | |
| MgSO4.7H2O | 2.0 | g/L | |
| 98% H2SO4 | 2.0 | mL/L | |
| Ferric ammonium citrate | 0.3 | g/L | |
| CaCl2.2H2O | 0.2 | g/L | |
| Yeast extract | 5.0 | g/L | |
| Trace metals | 5.0 | mL/L | |
| Glucose | 10.0 | g/L | |
| Carbenicillin | 100.0 | mg/L | |
The above media components were mixed together and the pH adjusted to 6.8 with NH4OH. The media was then filter sterilized.
Trace metals were used according to the following recipe:
| Citric acid, monohydrate | 4.0 | g/L | |
| MgSO4.7H2O | 3.0 | g/L | |
| MnSO4.H2O | 0.5 | g/L | |
| NaCl | 1.0 | g/L | |
| FeSO4.7H2O | 0.1 | g/L | |
| CoCl2.6H2O | 0.1 | g/L | |
| CaCl2 | 0.1 | g/L | |
| ZnSO4.7H2O | 0.1 | g/L | |
| CuSO4.5H2O | 10 | mg/L | |
| AlK(SO4)2.12H2O | 10 | mg/L | |
| H3BO3 | 10 | mg/L | |
| Na2MoO4.2H2O | 10 | mg/L | |
| NiSO4.6H2O | 10 | mg/L | |
| Na2SeO3 | 10 | mg/L | |
| Na2WO4.2H2O | 10 | mg/L | |
Cultures were started from seed culture inoculated from 50 μL frozen stock (15% glycerol as cryoprotectant) to 600 mL medium in a 2-L Erlenmeyer flask. Cultures were grown at 30°C C. in a shaker at 250 rpm for approximately 12 h and then used to seed the fermenter.
| Medium | |||
| KH2PO4 | 6.8 | g/L | |
| Citric acid | 2.0 | g/L | |
| MgSO4.7H2O | 2.0 | g/L | |
| 98% H2SO4 | 2.0 | mL/L | |
| Ferric ammonium citrate | 0.3 | g/L | |
| CaCl2.2H2O | 0.2 | g/L | |
| Mazu DF204 antifoam | 1.0 | mL/L | |
The above components were sterilized together in the fermenter vessel. The pH was raised to 6.7 with NH40H. Yeast extract (5 g/L) and trace metals solution (5 mL/L) were added aseptically from filter sterilized stock solutions. Glucose was added from 60% feed to give final concentration of 10 g/L. Carbenicillin was added at 100 mg/L. Volume after inoculation was 6 L.
The temperature was controlled at 36°C C. and the air flow rate was controlled at 6 standard liters per minute. Back pressure was controlled at 0.5 bar. The agitator was set at 350 rpm. Aqueous ammonia was used to control pH at 6.7. The glucose feed (60% glucose monohydrate) rate was controlled to maintain excess glucose.
The results of the fermentation run are given in Table 1.
| TABLE 1 | |||||
| EFT | OD550 | [Glucose] | [Glycerol] | Total Glucose | Total Glycerol |
| (hr) | (AU) | (g/L) | (g/L) | Fed (g) | Produced (g) |
| 0 | 0.8 | 9.3 | 25 | ||
| 6 | 4.7 | 4.0 | 2.0 | 49 | 14 |
| 8 | 5.4 | 0 | 3.6 | 71 | 25 |
| 10 | 6.7 | 0.0 | 4.7 | 116 | 33 |
| 12 | 7.4 | 2.1 | 7.0 | 157 | 49 |
| 14.2 | 10.4 | 0.3 | 10.0 | 230 | 70 |
| 16.2 | 18.1 | 9.7 | 15.5 | 259 | 106 |
| 18.2 | 12.4 | 14.5 | 305 | ||
| 20.2 | 11.8 | 17.4 | 17.7 | 353 | 119 |
| 22.2 | 11.0 | 12.6 | 382 | ||
| 24.2 | 10.8 | 6.5 | 26.6 | 404 | 178 |
| 26.2 | 10.9 | 6.8 | 442 | ||
| 28.2 | 10.4 | 10.3 | 31.5 | 463 | 216 |
| 30.2 | 10.2 | 13.1 | 30.4 | 493 | 213 |
| 32.2 | 10.1 | 8.1 | 28.2 | 512 | 196 |
| 34.2 | 10.2 | 3.5 | 33.4 | 530 | 223 |
| 36.2 | 10.1 | 5.8 | 548 | ||
| 38.2 | 9.8 | 5.1 | 36.1 | 512 | 233 |
Bulthuis, Ben A., Hsu, Amy Kuang-Hua, Gatenby, Anthony Arthur, Haynie, Sharon Loretta, Lareau, Richard D.
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